I know the thread is old but in case someone else ends up here too.
Rather than a zip file or another complicated work around I decided to simply do the following.
1. Import the main part of the book.
2. right click on the book and select "Open containing Folder"
3. Copy all extra files to the books directory.
4. Add a note to the description that there are supplementary materials, at whatever level of detail I deem appropriate for the book.
The files are with the book, and I only need to open the containing folder to get to them.
I use Cloud storage to get the files to other devices and the supplementary files go as well.
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